We, at Rishi Biotech, have developed few such tools that can be used for further interpretation. All one needs to do is select the appropriate tool from the list (view the documentation for the tools for detailed description), input the nucleotide or protein sequence as mentioned (in the specified format for each tool); and click on the 'Submit Query' button. The sequence is parsed to an appropriate program (mostly Perl Scripts) to handle the sequence and produce desired output.
The following gives a short description for the Analysis Tools available: (For complete information download the documentation here).
This tool takes input nucleotide sequence in GenBank / EMBL full file or sequence information, formats it to remove all unwanted spaces, tabs and numbers. The output is a formatted sequence alongwith other information as individual and total base counts, their percentages; AT, GT counts, their percentages; and their ratios.
This tool takes input nucleotide sequence in FASTA / GenBank / EMBL full file or sequence information, and computes the Open Reading Frames (starting with start codon ATG, ends with one of the stop codons) in all the 6 reading frames (i.e., +1, +2, +3, -1, -2, -3). The output is ORF information like start and end positions, the ORF length and the frame information.
This informative tool takes input protein sequence in FASTA / Swiss-Prot (submit sequence information only), analyses the protein and generates a variety of useful information like number and percentages of individual amino acids, number and percentages of amino acids based on their species, atomic constitution (numbers and percentages) and finally generates two formulae for the protein based on its atomic constituents and also amino acid constituents.
When we input nucleotide sequence in FASTA / GenBank / EMBL full file or sequence information, and select the Restriction enzyme of choice from the options in the following page, this tool carries out a virtual restriction digestion and displays all the fragments so generated. Additional information like starting and cleavage points and length of each fragment are also mentioned in the output.